This class stores a list of predicted reflections for a monochromatic
X-ray crystallographic rotation image. The class has methods for
adding/deleting reflections, sorting the reflection list and
calculating which spots will be spatially overlapped for a given
spot size. In general, reflections are handled as JdlPredictedReflection
objects.

This section has methods to clear the list and to add/delete/insert
replace reflections in the list. It also includes a method to replace
reflection indices when a relection is put into an asymmetric unit.

This method replaces the current reflection indices with those
required (normally those converted to an asymmetric unit) and
sets the symmetry operator number (normally that required to
convert the indices to those in the asymmetric unit). The
other likely use is to reverse this procedure.

Method Definition:

public void putHKL (int iref, int h, int k, int l, int ksym)

Parameters List:

iref

The position within the list of the reflection for which
the indices are to be reset (reflection positions numbered from 1 upwards).

h

The new 'h' index.

k

The new 'k' index.

l

The new 'l' index.

ksym

The symmetry operator number used to generate the indices
or 0 to unset this item (see JdlPredictedReflection class for
further details).

This method returns the number of spatially overlapped reflections currently
in the reflection list for a selected crystal and image number. The
spatial overlaps must have been calculated using the setSpatialOverlaps(..)
method directly or via the predictReflections(..) method with 'spat' set
to true;

Method Definition:

public int getNumberOfSpatialOverlaps(int icrys, int imgnum)

Parameters List:

icrys

The selected crystal number (-1 = all crystal numbers).

imgnum

The selected image number (-1 = all image numbers).

Method Return:

The number of reflections in the list for the requested crystal
and image.

This method determines the spatially overlapped reflections (and
sets an internal flag) for the reflections of a given crystal and
image. The overlap criterion is based on the given spot diameter.
The number of spatially overlapped spots is returned.

Method Definition:

public int setSpatialOverlaps (int icrys, int img_id, double spotd)

Parameters List:

icrys

The selected crystal number.

img_id

The selected image number or identifier as stored when
the spot list was predicted.

This method predicts and stores a reflection list using the parameters
stored in a JdlDiffractionDataModule object. Note that the image
identifiers stored may be found from the range and image numbers
using the JdlDiffractionDataModule.setImageID(..) method.

The JdlDiffractionDataModule object containing the detector and
crystal data.

iset

The set number within the Diffraction Data Module.

irange

The rotation range number.

imgnum

The number of the image from 1 up (within the requested rotation
range) for which the prediction is to be carried out.

quick

If set to true a quick prediction will be carried out with
fewer details being calculated for each reflection. If false the full
detailed prediction will be performed (see the parameters of the
JdlRotReflOutputHandler outputPredictedReflection(..) method for details
of the items which are calculated.

recorded

If true, store only reflections flagged as being recorded.
If false include predicted but non-recorded reflections.

spat

If true calculate spatial overlap flags after generating the
reflection list, if false do not.

append

If true, append the reflections to any reflections already
stored. If false clear any stored reflections before creating the list.

This method predicts and stores a reflection list using the parameters
stored in JdlPositionedDetector and JdlPositionedCrystal objects.
Note that the image identifiers stored may be found from the range and
image numbers using the JdlDiffractionDataModule.setImageID(..) method.

A JdlPositionedDetector object containing details of the
positioned detector, gonioneter and X-ray source.

poscrys

A JdlPositionedCrystal containing details of the crystal cell,
symmetry and setting.

icrys

The crystal number (The image may be identified by the
crystal number and image number).

irange

A rotation range number for which 'rotstart' is the start
angle.

rotstart

The start rotation angle in degrees (see also imgnum).

oscang

The oscillation angle in degrees.

imgnum

The number of the image for which the prediction is
to be carried out from 1 up (The rotation range used will be from
rotstart + (imgnum-1)*oscang to rotstart + imgnum*oscang).

rmin

Minimum radius for prediction in mm.

xmin

Minimum 'x' limit for prediction in mm (ignored if xmin = xmax)

xmax

Maximum 'x' limit for prediction in mm (ignored if xmax = xmin)

ymin

Minimum 'y' limit for prediction in mm (ignored if ymin = ymax)

ymax

Maximum 'y' limit for prediction in mm (ignored if ymax = ymin)

quick

If set to true a quick prediction will be carried out with
fewer details being calculated for each reflection. If false the full
detailed prediction will be performed (see the parameters of the
JdlRotReflOutputHandler outputPredictedReflection(..) method for details
of the items which are calculated.

recorded

If true, store only reflections flagged as being recorded.
If false include predicted but non-recorded reflections.

spat

If true calculate spatial overlap flags after generating the
reflection list, if false do not.

append

If true, append the reflections to any reflections already
stored. If false clear any stored reflections before creating the list.

This method predicts and stores a reflection list using the parameters
stored in a JdlDiffractionDataModule object. The prediction is carried out
for a set of images covering a given rotation range. A fully detailed
prediction is carried out and only the data for recorded reflections are
stored. Note that the image identifiers stored may be found from the range
and image numbers using the JdlDiffractionDataModule.setImageID(..) method.
The generated reflections are added to any currently in the reflections list.

The JdlDiffractionDataModule object containing the detector and
crystal data.

iset

The set number within the Diffraction Data Module.

irange

The rotation range number.

setting_opt

This determines the exact setting parameters used for
each image prediction:
= 0, Use the setting parameters defined for the first image of the
complete dataset
= 1, Use the setting parameters defined for the first image of the
specified range
= 2, Use the setting parameters defined for each individual image
Note that, in most cases, it is likely that the setting parameters for
all images of the set will in fact be identical.

spat

If true calculate spatial overlap flags after generating the
reflection list, if false do not.

This method predicts and stores a reflection list using the parameters
stored in JdlPositionedDetector and JdlPositionedCrystal objects.
The prediction is carried out for a set of images covering a given
rotation range. A fully detailed prediction is carried out and only the
data for recorded reflections are stored. Note that the image identifiers
stored may be found from the range and image numbers
using the JdlDiffractionDataModule.setImageID(..) method. The generated
reflections are added to any currently in the reflections list.